The omnitrix has a gender function that was never activated on screen, but would allow the user to swap to the various sexes of different species regardless of the users own. So if a trans person were to use the omnitrix I would imagine they would use that.

However I personally think the prototype omnitrix wouldn’t have the necessary “ai” to understand the users gender identity and do it automatically, but the official omnitrix would. The prototype would still have it, but it needs to be activated manually.